Michael I. Jordan

Bio: Michael I. Jordan is an academic researcher from University of California, Berkeley. The author has contributed to research in topics: Computer science & Inference. The author has an hindex of 176, co-authored 1016 publications receiving 216204 citations. Previous affiliations of Michael I. Jordan include Stanford University & Princeton University.

A Hierarchical Bayesian Markovian Model for Motifs in Biopolymer Sequences

Abstract: We propose a dynamic Bayesian model for motifs in biopolymer sequences which captures rich biological prior knowledge and positional dependencies in motif structure in a principled way. Our model posits that the position-specific multinomial parameters for monomer distribution are distributed as a latent Dirichlet-mixture random variable, and the position-specific Dirichlet component is determined by a hidden Markov process. Model parameters can be fit on training motifs using a variational EM algorithm within an empirical Bayesian framework. Variational inference is also used for detecting hidden motifs. Our model improves over previous models that ignore biological priors and positional dependence. It has much higher sensitivity to motifs during detection and a notable ability to distinguish genuine motifs from false recurring patterns.

A Swiss Army Infinitesimal Jackknife

Abstract: The error or variability of machine learning algorithms is often assessed by repeatedly refitting a model with different weighted versions of the observed data. The ubiquitous tools of cross-validation (CV) and the bootstrap are examples of this technique. These methods are powerful in large part due to their model agnosticism but can be slow to run on modern, large data sets due to the need to repeatedly re-fit the model. In this work, we use a linear approximation to the dependence of the fitting procedure on the weights, producing results that can be faster than repeated re-fitting by an order of magnitude. This linear approximation is sometimes known as the “infinitesimal jackknife” in the statistics literature, where it is mostly used as a theoretical tool to prove asymptotic results. We provide explicit finite-sample error bounds for the infinitesimal jackknife in terms of a small number of simple, verifiable assumptions. Our results apply whether the weights and data are stochastic or deterministic, and so can be used as a tool for proving the accuracy of the infinitesimal jackknife on a wide variety of problems. As a corollary, we state mild regularity conditions under which our approximation consistently estimates true leave k-out cross-validation for any fixed k. These theoretical results, together with modern automatic differentiation software, support the application of the infinitesimal jackknife to a wide variety of practical problems in machine learning, providing a “Swiss Army infinitesimal jackknife.” We demonstrate the accuracy of our methods on a range of simulated and real datasets.

Statistical modeling of biomedical corpora: mining the Caenorhabditis Genetic Center Bibliography for genes related to life span

Abstract: The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here, the potential of such modeling is demonstrated by examining the 5,225 free-text items in the Caenorhabditis Genetic Center (CGC) Bibliography using techniques from statistical information retrieval. Items in the CGC biomedical text corpus were modeled using the Latent Dirichlet Allocation (LDA) model. LDA is a hierarchical Bayesian model which represents a document as a random mixture over latent topics; each topic is characterized by a distribution over words. An LDA model estimated from CGC items had better predictive performance than two standard models (unigram and mixture of unigrams) trained using the same data. To illustrate the practical utility of LDA models of biomedical corpora, a trained CGC LDA model was used for a retrospective study of nematode genes known to be associated with life span modification. Corpus-, document-, and word-level LDA parameters were combined with terms from the Gene Ontology to enhance the explanatory value of the CGC LDA model, and to suggest additional candidates for age-related genes. A novel, pairwise document similarity measure based on the posterior distribution on the topic simplex was formulated and used to search the CGC database for "homologs" of a "query" document discussing the life span-modifying clk-2 gene. Inspection of these document homologs enabled and facilitated the production of hypotheses about the function and role of clk-2. Like other graphical models for genetic, genomic and other types of biological data, LDA provides a method for extracting unanticipated insights and generating predictions amenable to subsequent experimental validation.

Generalized Momentum-Based Methods: A Hamiltonian Perspective

Abstract: We take a Hamiltonian-based perspective to generalize Nesterov's accelerated gradient descent and Polyak's heavy ball method to a broad class of momentum methods in the setting of (possibly) constrained minimization in Euclidean and non-Euclidean normed vector spaces. Our perspective leads to a generic and unifying nonasymptotic analysis of convergence of these methods in both the function value (in the setting of convex optimization) and in norm of the gradient (in the setting of unconstrained, possibly nonconvex, optimization). Our approach relies upon a time-varying Hamiltonian that produces generalized momentum methods as its equations of motion. The convergence analysis for these methods is intuitive and is based on the conserved quantities of the time-dependent Hamiltonian.

Online control of the false discovery rate with decaying memory

Abstract: In the online multiple testing problem, p-values corresponding to different null hypotheses are presented one by one, and the decision of whether to reject a hypothesis must be made immediately, after which the next p-value is presented. Alpha-investing algorithms to control the false discovery rate were first formulated by Foster and Stine and have since been generalized and applied to various settings, varying from quality-preserving databases for science to multiple A/B tests for internet commerce. This paper improves the class of generalized alpha-investing algorithms (GAI) in four ways : (a) we show how to uniformly improve the power of the entire class of GAI procedures under independence by awarding more alpha-wealth for each rejection, giving a near win-win resolution to a dilemma raised by Javanmard and Montanari, (b) we demonstrate how to incorporate prior weights to indicate domain knowledge of which hypotheses are likely to be null or non-null, (c) we allow for differing penalties for false discoveries to indicate that some hypotheses may be more meaningful/important than others, (d) we define a new quantity called the \emph{decaying memory false discovery rate, or $\memfdr$} that may be more meaningful for applications with an explicit time component, using a discount factor to incrementally forget past decisions and alleviate some potential problems that we describe and name ``piggybacking'' and ``alpha-death''. Our GAI++ algorithms incorporate all four generalizations (a, b, c, d) simulatenously, and reduce to more powerful variants of earlier algorithms when the weights and decay are all set to unity.

Going deeper with convolutions

Abstract: We propose a deep convolutional neural network architecture codenamed Inception that achieves the new state of the art for classification and detection in the ImageNet Large-Scale Visual Recognition Challenge 2014 (ILSVRC14). The main hallmark of this architecture is the improved utilization of the computing resources inside the network. By a carefully crafted design, we increased the depth and width of the network while keeping the computational budget constant. To optimize quality, the architectural decisions were based on the Hebbian principle and the intuition of multi-scale processing. One particular incarnation used in our submission for ILSVRC14 is called GoogLeNet, a 22 layers deep network, the quality of which is assessed in the context of classification and detection.

Deep Learning

Abstract: Deep learning is a form of machine learning that enables computers to learn from experience and understand the world in terms of a hierarchy of concepts. Because the computer gathers knowledge from experience, there is no need for a human computer operator to formally specify all the knowledge that the computer needs. The hierarchy of concepts allows the computer to learn complicated concepts by building them out of simpler ones; a graph of these hierarchies would be many layers deep. This book introduces a broad range of topics in deep learning. The text offers mathematical and conceptual background, covering relevant concepts in linear algebra, probability theory and information theory, numerical computation, and machine learning. It describes deep learning techniques used by practitioners in industry, including deep feedforward networks, regularization, optimization algorithms, convolutional networks, sequence modeling, and practical methodology; and it surveys such applications as natural language processing, speech recognition, computer vision, online recommendation systems, bioinformatics, and videogames. Finally, the book offers research perspectives, covering such theoretical topics as linear factor models, autoencoders, representation learning, structured probabilistic models, Monte Carlo methods, the partition function, approximate inference, and deep generative models. Deep Learning can be used by undergraduate or graduate students planning careers in either industry or research, and by software engineers who want to begin using deep learning in their products or platforms. A website offers supplementary material for both readers and instructors.

Reinforcement Learning: An Introduction

Abstract: Reinforcement learning, one of the most active research areas in artificial intelligence, is a computational approach to learning whereby an agent tries to maximize the total amount of reward it receives when interacting with a complex, uncertain environment. In Reinforcement Learning, Richard Sutton and Andrew Barto provide a clear and simple account of the key ideas and algorithms of reinforcement learning. Their discussion ranges from the history of the field's intellectual foundations to the most recent developments and applications. The only necessary mathematical background is familiarity with elementary concepts of probability. The book is divided into three parts. Part I defines the reinforcement learning problem in terms of Markov decision processes. Part II provides basic solution methods: dynamic programming, Monte Carlo methods, and temporal-difference learning. Part III presents a unified view of the solution methods and incorporates artificial neural networks, eligibility traces, and planning; the two final chapters present case studies and consider the future of reinforcement learning.

Latent dirichlet allocation

Abstract: We describe latent Dirichlet allocation (LDA), a generative probabilistic model for collections of discrete data such as text corpora. LDA is a three-level hierarchical Bayesian model, in which each item of a collection is modeled as a finite mixture over an underlying set of topics. Each topic is, in turn, modeled as an infinite mixture over an underlying set of topic probabilities. In the context of text modeling, the topic probabilities provide an explicit representation of a document. We present efficient approximate inference techniques based on variational methods and an EM algorithm for empirical Bayes parameter estimation. We report results in document modeling, text classification, and collaborative filtering, comparing to a mixture of unigrams model and the probabilistic LSI model.

Latent Dirichlet Allocation

Abstract: We propose a generative model for text and other collections of discrete data that generalizes or improves on several previous models including naive Bayes/unigram, mixture of unigrams [6], and Hof-mann's aspect model, also known as probabilistic latent semantic indexing (pLSI) [3]. In the context of text modeling, our model posits that each document is generated as a mixture of topics, where the continuous-valued mixture proportions are distributed as a latent Dirichlet random variable. Inference and learning are carried out efficiently via variational algorithms. We present empirical results on applications of this model to problems in text modeling, collaborative filtering, and text classification.